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[Selection Panel]

Selection is defined as using the mouse to single out one or more objects such as atoms, molecules, surfaces, contours, bonds, or vectors in order to perform an operation on them. Objects may be chosen individually or in groups by enlarging the picking are via the preferences menu. Selection is accomplished by putting the cursor on the object and pushing the left mouse button. The particular operation takes effect when the "QUIT" button is pushed. The selection options are:

  • ATOM LABELS: Toggle labeling or unlabeling of one or more atoms.


  • BOND LABELS: Toggle labeling or unlabeling of one or more bonds.


  • CEN. OF GEO. : After one or more atoms are selected, pressing the "C" key redefines the rotational axis about the points selected. All atoms must be in the same molecule. If no atoms are selected and the "C" key is pressed, the center of geometry for the entire system is recalculated if the current object setting is "ALL" (see objects ) . If one molecular object is currently selected only its center of geometry is recalculated.


  • PICK POINTS : Pick a point on a graph and go to that step. When QMView displays sequences of coordinates such as for MD, IRC or optimization runs, graphcs can also be displayed depicting properties such as the energy or the RMS gradient as a function of the coordinate set. The user may select a point on the graph and that set will be displayed.


  • ROT. AXIS : Picking two atoms results in a rotational axis being defined along the line (using XY-ROT from the translation menu ).


  • ROT. PLANE : Picking three atoms results in a rotational axis perpendicular to the defined plane (using XY-ROT from the translation menu. ).


  • COMBINE : Picking two atoms, each in a different molecule results in combining the two molecules into one.


  • SEPARATE : Picking atoms from a single molecule and pressing the "C" key results in the selected atoms being defined as a new molecule.


  • REPLACE : Picking an atom allows the user to replace it with a different atom type.


  • REMOVE: Picking an atom from a molecule removes that molecule.


  • DELETE: delete individual atoms from a molecule.


  • ATOMLIST : Picking two atoms labels all atoms along the bond chain in that direction. This was for debugging the bond chain list that is used for changing bonds, angles and torsions (see below).


  • SYMMETRY : Picking an atom results in printing out the symmetry groups that the structure could belong to.

  • ALIGN : Align two molecules based on 3 atoms from each molecule. Atoms are chosen by picking corresponding atoms on each molecule: e.g. atom 1 on molecule 1, atom 1 on molecule 2 etc. The user may then have QMView calculate surfaces that represent the differences between two sets of volumetric data. (see structure alignment ).

  • ADD BOND : Picking two atoms draws a bond between them.


  • DEL. BOND : Picking a bond deletes that bond.


  • ADD ANG. MEAS. : Picking three atoms displays the angle measurement in degrees.


  • DEL ANG. MEAS. : Picking an angle deletes the measurement display.


  • CHANGE BOND : If two atoms from an already defined bond or a bond itself is picked, the user is prompted for a bond length. If none is selected and "QUIT" is chosen, an interactive transformation is defined (using "XY-TRAN" from the translation menu). NOTE: QMView only allows one internal transformation to be defined at one time.


  • FIX BOND : Picking a bond that has been selected with CHANGE BOND fixes that bond at that length and removes the internal transformation.


  • CHANGE ANGLE : When three atoms are picked, the user is prompted for an angle value in degrees. If none is selected and "QUIT" is chosen, an interactive transformation is defined (using "XY-ROT" from the translation menu).


  • FIX ANGLE : Picking an angle that has been selected with CHANGE ANGLE fixes that angle at that value and removes the internal transformation.


  • ADD TORS. MEAS. : Picking four atoms displays the torsion angle measurement in degrees.


  • DEL TORS. MEAS. : Picking a torsion angle deletes the measurement display.


  • DEL ANG. MEAS. : Picking an angle deletes the measurement display.


  • CHANGE TORS. : When four atoms are picked, the user is prompted for an torsion value in degrees. If none is selected and "QUIT" is chosen, an interactive transformation is defined (using "XY-ROT" from the translation menu).


  • FIX TORS. : Picking a torsion angle that has been selected with CHANGE TORS. fixes that torsion angle at that value and removes the internal transformation.


  • ADD VECTOR: Picking an atom displays the corresponding vector, if vector data is available. If the vector is already displayed, its magnitude is toggled.


  • DELELTE VECOTR: Picking a vector deletes it from the display.


  • ADD CONTOURS : When planar contours are displayed, picking on one adds that contour to the display list. This option allows for the display of more then one contour.


  • DELETE CONTOURS : Deletes a contour from the display list.



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